Pankaj Trivedi

Colorado State University | CSU · Department of Agricultural Biology

The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome‐oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence—a comparison between rhizosphere and bulk soil samples—on bacterial, fungal, protists and invert...

Plant-soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional...

The rhizosphere influence on the soil microbiome and function of crop wild progenitors remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence – a comparison between rhizosphere and bulk soil samples – on bacterial, fungal, protists and invertebr...

Greenspaces are important for sustaining healthy urban environments and their human populations. Yet their capacity to support multiple ecosystem services simultaneously (multiservices) compared with nearby natural ecosystems remains virtually unknown. We conducted a global field survey in 56 urban areas to investigate the influence of urban greens...

Introduction The application of host‐derived antibacterial peptides has been highlighted as a potential efficacious and safe tool for the treatment of Huanglongbing (HLB), the most devastating disease of citrus. However, pathogenic bacteria such as HLB‐causing Candidatus liberibacter asiaticus ( C Las) often develop resistance against the host anti...

The rewilding of modern agriculture is challenged by our current uncertainties on the microbiome of major crop wild progenitors (CWPs). Here, we conducted the first global standardised field survey to investigate the edaphoclimatic conditions and soil microbiome of 125 wild populations associated with 10 of the most important CWPs at their centres...

Soil is one of the largest reservoirs for antibiotic resistance in the world. Bacteria can carry antibiotic resistance genes (ARGs) and share them via mechanisms like mobile genetic elements. Antibiotic resistance in the soil microbes impacts microbial community dynamics and it can spread to human and animal pathogens. Despite this importance, this...

The decomposition of litter and the supply of nutrients into and from the soil are two fundamental processes through which the above and belowground world interact. Microbial biodiversity, and especially that of decomposers, plays a key role in these processes by helping litter decomposition. Yet the relative contribution of litter diversity and so...

Salt stress induced ethylene emission from plants regulates diverse arrays of functionalities and ethylene levels can be decreased by the inoculation of 1-aminocyclopropane-1-carboxylic acid ACC deaminase (ACCD) pro- ducing methylotrophic bacteria that is important for enhancing plant biomass and stress tolerance. This study was conducted to evalua...

Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socioeconomic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution a...

Soil mosses are among the most widely distributed organisms on land. Experiments and observations suggest that they contribute to terrestrial soil biodiversity and function, yet their ecological contribution to soil has never been assessed globally under natural conditions. Here we conducted the most comprehensive global standardized field study to...

Pathogenesis-related (PR) signaling plays multiple roles in plant development under abiotic and biotic stress conditions and is regulated by a plethora of plant physiologi- cal as well as external factors. Here, our study was conducted to evaluate the role of an ACC deaminase-producing endophytic bacteria in regulating ethylene-induced PR signaling...

Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil c...

Urban greenspaces support multiple nature-based services, many of which depend on the amount of soil carbon (C). Yet, the environmental drivers of soil C and its sensitivity to warming are still poorly understood globally. Here we use soil samples from 56 paired urban greenspaces and natural ecosystems worldwide and combine soil C concentration and...

While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities a...

Background Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth’s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and...

The importance of host‐associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the...

Soils are the foundation of all terrestrial ecosystems1. However, unlike for plants and animals, a global assessment of hotspots for soil nature conservation is still lacking2. This hampers our ability to establish nature conservation priorities for the multiple dimensions that support the soil system: from soil biodiversity to ecosystem services....

Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can signif...

Background Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth’s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and...

Introduction Harnessing synthetic communities (SynCom) of plant growth-promoting (PGP) microorganisms is considered a promising approach to improve crop fitness and productivity. However, biotic mechanisms that underpin improved plant performance and the effects of delivery mode of synthetic community are poorly understood. These are critical knowl...

Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can signif...

The frequency and severity of drought are increasing due to anthropogenic climate change and are already limiting cropping system productivity in many regions around the world. Few microbial groups within plant microbiomes can potentially contribute towards the fitness and productivity of their hosts under abiotic stress events including water defi...

Soil-borne fungal phytopathogens are important threats to soil and crop health. However, their community composition and environmental determinants remain unclear. Here, we explored the effects of agricultural fertilization regime (i.e., organic material application) on soil fungal phytopathogens, using data sets from a combination of field survey...

The environmental factors controlling soil biodiversity along resource gradients remain poorly understood in wet tropical ecosystems. Aboveground biodiversity is expected to be driven by changes in nutrient availability in these ecosystems, however, much less is known about the importance of nutrient availability in driving soil biodiversity. Here,...

The structure and function of the soil microbiome of urban greenspaces remain largely undetermined. We conducted a global field survey in urban greenspaces and neighboring natural ecosystems across 56 cities from six continents, and found that urban soils are important hotspots for soil bacterial, protist and functional gene diversity , but support...

ACC deaminase (ACCD) containing plant growth promoting (PGP) bacteria play an imperative role in curbing the stress mediated ethylene and associated adverse effects on plant growth and productivity. We put forth here, a new dimension in stress amelioration machinery by using an ACCD+ multifaceted PGP Methylobacterium oryzae CBMB20 in enhancing cell...

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhiz...

A Correction to this paper has been published: https://doi.org/10.1038/s41579-020-00490-8

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A global assessment of the structure and function of the crop microbiome is urgently needed for the development of effective and rationally designed microbiome technologies for sustainable agriculture. Such an effort will provide new knowledge on the key ecological and evolutionary interactions between plant species and their microbiomes that can b...

The importance of soil age as an ecosystem driver across biomes remains largely unresolved. By combining a cross-biome global field survey, including data for 32 soil, plant, and microbial properties in 16 soil chronosequences, with a global meta-analysis, we show that soil age is a significant ecosystem driver, but only accounts for a relatively s...

Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how...

The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable m...

The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Here, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria,...

Host microbiomes play a critical role in host fitness and health. Whilst the current ‘holobiont’ concept framework has greatly expanded eco‐evolutionary and functional understanding of host‐microbiome interactions, the important role of biotic interactions and microbial loop (compositional linkage between soil, plant, animal) in shaping host‐microb...

Unlike plants and vertebrates, the ecological preferences, and potential vulnerabilities of soil invertebrates to environmental change, remain poorly understood in terrestrial ecosystems globally. We conducted a cross‐biome survey including 83 locations across six continents to advance our understanding of the ecological preferences and vulnerabili...

Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using 13C-glucose labeling. Here we show...

Background: The diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genus Eucalyptus (family Myrtaceae). Eucalyptus produces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist,...

The Australian sugarcane industry is facing a new threat of the currently undiagnosed Yellow Canopy Syndrome (YCS). Here, we investigated if YCS is linked to detrimental shifts in soil microbial function and/or altered physico-chemical soil properties. We examined changes in rhizosphere soil microbial assemblages, functional gene profiles and micro...

Competition can be fully hierarchical or intransitive, and this degree of hierarchy is driven by multiple factors, including environmental conditions, the functional traits of the species involved or the topology of competition networks. Studies simultaneously analysing these drivers of competition hierarchy are rare. Additionally, organisms compet...

The technical comment from Sanderman provides a unique opportunity to deepen our understanding of the mechanisms explaining the role of paleoclimate in the contemporary distribution of global soil C content, as reported in our article. Sanderman argues that the role of paleoclimate in predicting soil C content might be accounted for by using slowly...

Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop mi...

Uncovering potential soil drivers of soils pathogen suppression represent an essential step in order to develop alternative and sustainable management strategies for disease control and increased soil health. In this study, we tested the potential role of keystone microbial taxa and chemical/physical properties in the suppression (referred to as so...

Plant-associated microbiomes have tremendous potential to improve plant resilience and yields in farming systems. There is increasing evidence that biological technologies that use microbes or their metabolites can enhance nutrient uptake and yield, control pests and mitigate plant stress responses. However, to fully realize the potential of microb...

Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes i...

Pathogens from the fastidious, phloem-restricted 'Candidatus Liberibacter' species cause the devastating Huanglongbing (HLB) disease in citrus worldwide and cause diseases on many solanaceous crops and plants in the Apiaceae family. However, little is known about the pathogenic mechanisms due to the difficulty in culturing the corresponding Liberib...

Globally, drylands represent the largest terrestrial biome and are projected to expand by 23% by the end of this century. Drylands are characterized by extremely low levels of water and nutrients and exhibit highly heterogeneous distribution in plants and biocrusts which make microbial processes shaping the dryland functioning rather unique compare...

The phytobiome is composed of plants, their environment, and diverse interacting microscopic and macroscopic organisms, which together influence plant health and productivity. These organisms form complex networks that are established and regulated through nutrient cycling, competition, antagonism, and chemical communication mediated by a diverse a...

Climatic conditions shift gradually over millennia, altering the rates at which carbon (C) is fixed from the atmosphere and stored in the soil. However, legacy impacts of past climates on current soil C stocks are poorly understood. We used data from more than 5000 terrestrial sites from three global and regional data sets to identify the relative...

Soil carbon (C) stabilisation is known to depend in part on its distribution in structural aggregates, and upon soil microbial activity within the aggregates. However, the mechanisms and relative contributions of different microbial groups to C turnover in different aggregates under various management practices remain unclear. The aim of this study...

Microbiome and the future for food and nutrient security.

Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus (Ca.) Phytoplasma sp...

Despite the vital role of microorganisms for ecosystem functioning and human welfare, our understanding of their global diversity and biogeographical patterns lags significantly behind that of plants and animals. We conducted a meta- Analysis including ~600 soil samples from all continents to evaluate the biogeographical patterns and drivers of bac...

Agricultural intensification is placing tremendous pressure on the soil’s capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major adv...

A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extra...

Despite the vital role of microorganisms for ecosystem functioning and human welfare, our understanding of their global diversity and biogeographical patterns lags significantly behind that of plants and animals. We conducted a meta-analysis including ~600 soil samples from all continents to evaluate the biogeographical patterns and drivers of bact...

Key messages • Soil is an important habitat for thousand millions of organisms. • Soil biodiversity is extremely diverse in shapes, colours, sizes and functions. • Soil biodiversity is globally distributed, from deserts to polar regions through grasslands, forests, urban and agricultural areas. • Soil biodiversity supports many services essential t...

SPE EA Pôle BIOME The Atlas is divided in 8 chapters covering all the aspects of soil biodiversity: - Chapter I: The soil habitat - Chapter II: Diversity of soil organisms - Chapter III: Geographical and temporal distribution - Chapter IV: Ecosystem functions and services - Chapter V: Threats - Chapter VI: Interventions - Chapter VII: Policy, educa...

Huanglongbing (HLB) is currently the most economically devastating disease of citrus worldwide and no established cure is available. Defense inducing compounds have been widely used in agriculture to protect plants from pathogens by activating the plant immune system. In this study the effects of various chemical inducers on HLB diseased citrus wer...

Understanding the influence of long-term crop management practices on the soil microbial community is critical for linking soil microbial flora with ecosystem processes such as those involved in soil carbon cycling. In this study, pyrosequencing and a functional gene array (GeoChip 4.0) were used to investigate the shifts in microbial composition a...

Understanding the influence of long-term crop management practices on the soil microbial community is critical for linking soil microbial flora with ecosystem processes such as those involved in soil carbon cycling. In this study, pyrosequencing and a functional gene array (GeoChip 4.0) were used to investigate the shifts in microbial composition a...

Terrestrial arid and semiarid ecosystems (drylands) constitute about 41% of Earth's land surface, and are predicted to experience increasing fluctuations in water and nitrogen availability. Mounting evidence has confirmed the significant importance of ammonia oxidizing archaea (AOA) and bacteria (AOB) in nitrification, plant nitrogen availability,...

Pathogens face a hostile and often novel environment when infecting a new host, and adaptation is likely to be an important determinant of the success in colonization and establishment. We hypothesized that resistant hosts will impose stronger selection on pathogens than susceptible hosts, which should accelerate pathogen evolution through selectio...

Pathogens face a hostile and often novel environment when infecting a new host, and adaptation is likely to be an important determinant of the success in colonization and establishment. We hypothesized that resistant hosts will impose stronger selection on pathogens than susceptible hosts, which should accelerate pathogen evolution through selectio...

Soil organic carbon performs a number of functions in ecosystems and it is clear that microbial communities play important roles in land-atmosphere carbon (C) exchange and soil C storage. In this review, we discuss microbial modulators of soil C storage, 'omics'-based approaches to characterize microbial system interactions impacting terrestrial C...

Citrus huanglongbing (HLB) is one of the oldest citrus diseases and has been known for over a century. HLB is caused by Candidatus Liberibacter spp. that are phloem-limited fastidious α-proteobacteria and infect hosts in different Kingdoms (i.e., Animalia and Plantae). When compared to well-characterized, cultivatable plant pathogenic Gram-negative...

Huanglongbing is the most devastating disease of citrus caused by Candidatus Liberibacter asiaticus (Las). In the present study, we report the discovery of novel small molecule inhibitors against SecA ATPase of Las by using structure based design methods. We built the homology model of SecA protein structure of Las based on the SecA of Escherichia...

While microorganisms are ubiquitous in nature, their distribution is governed by environmental specificities. The use of biological fertilizers, in recent times, has received well deserved attention mainly due to increased global preference for natural “organic” products, as well as to reduce the load of chemical fertilizers on the environment. Two...

The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how 'Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associat...

Cultivable diversity of bacteria associated with citrus was investigated as part of a larger study to understand the roles of beneficial bacteria and utilize them to increase the productive capacity and sustainability of agro-ecosystems. Citrus roots from Huanglongbing (HLB) diseased symptomatic and asymptomatic citrus were used in this study. A to...

Soil samples, collected after the fire operations at agricultural sites under shifting cultivation in northeast India, were subjected to physico-chemical and microbial analysis. The fire affected various physico-chemical properties of the soil. Significant differences in pH and electrical conductivity were recorded in soil of fired and fallow plots...

To examine the effect of pathogens on the diversity and structure of plant-associated bacterial communities, we carried out a molecular analysis using citrus and huanglongbing as a host-disease model. 16S rRNA gene clone library analysis of citrus roots revealed shifts in microbial diversity in response to pathogen infection. The clone library of t...

A study was undertaken to determine the free-living culturable diazotrophic bacteria of paddy soils from a long-term fertilizer management experiment. Long-term application of different fertilizers significantly affected the population of free-living diazotrophs. Out of 165 distinct bacterial morphotypes observed during the isolation process, only...

Seventy-eight isolates of actinomycetes were isolated from the soil samples collected from alpine zones of Pindari glacier region in Indian Himalaya. Following a plate based rapid screening using two test fungi, five efficient isolates (nos. HA1, HA2, HA6, HA40, and HA142) were selected for further characterization with special reference to their a...

Citrus Huanglongbing (HLB) is a devastating disease of citrus known to be associated with a fastidious, phloem-limited Gram-negative, yet to be cultured bacterium in the genus Candidatus Liberibacter. In the present study we have developed a method to quantify viable Candidatus Liberibacter asiaticus (Las) with the aid of ethidium monoazide (EMA) w...